title: G4 motifs correlate with promoter-proximal transcriptional pausing in human genes.
abstract: The RNA Pol II transcription complex pauses just downstream of the promoter in a significant fraction of human genes. The local features of genomic structure that contribute to pausing have not been defined. Here, we show that genes that pause are more G-rich within the region flanking the transcription start site (TSS) than RefSeq genes or non-paused genes. We show that enrichment of binding motifs for common transcription factors, such as SP1, may account for G-richness upstream but not downstream of the TSS. We further show that pausing correlates with the presence of a GrIn1 element, an element bearing one or more G4 motifs at the 5'-end of the first intron, on the non-template DNA strand. These results suggest potential roles for dynamic G4 DNA and G4 RNA structures in cis-regulation of pausing, and thus genome-wide regulation of gene expression, in human cells.
authors.affiliation: Molecular and Cellular Biology Graduate Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
authors.forename: Johanna
authors.initials: J
authors.lastname: Eddy
authors.forename: Aarthy C
authors.initials: AC
authors.lastname: Vallur
authors.forename: Sudir
authors.initials: S
authors.lastname: Varma
authors.forename: Hongfang
authors.initials: H
authors.lastname: Liu
authors.forename: William C
authors.initials: WC
authors.lastname: Reinhold
authors.forename: Yves
authors.initials: Y
authors.lastname: Pommier
authors.forename: Nancy
authors.initials: N
authors.lastname: Maizels
mesh_terms: D001665:Binding Sites; D045744:Cell Line, Tumor; D018899:CpG Islands; D006147:Guanine / Q000032:analysis*; D034441:Heterogeneous-Nuclear Ribonucleoproteins / Q000378:metabolism; D006801:Humans; D007438:Introns; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D034441:Heterogeneous-Nuclear Ribonucleoproteins; D014157:Transcription Factors; D006147:Guanine; D012319:RNA Polymerase II